Minor difficulty here--we aren't entirely sure of the phonetic values of either script (and in the case of the Phaistos disk, whether it's partially logographic and partially phonetic a la the Mayan heiroglyphs or the use of kanji in practice), whilst this program is more useful in reconstructing protolanguages (ancestral reconstructed languages) of languages that have been spoken in recent enough history that they got recorded in SOME format.

That said--the Indus script of Mohenjo Daro is theorised to be from SOME Dravidian or Indo-Aryan language now since lost, so it may be useful in reconstructing a proto-language that might work in decoding the script. Part of the difficulty is that literally the script is so old that we have almost nothing to compare to it--the only other older script would be Sumerian, and there are maybe two loan words in Sumerian that point to a possible Indo-Aryan language origin--and part of the issue is that it's logosyllabic like kanji--sometimes a symbol means, well, a word, sometimes it means a syllable, and those types of scripts tend to be more difficult to "reverse engineer" than a purely syllabic or alphabetic script.

Phaistos is a little more difficult because there's questions on whether the script is purely phonetic (if it is, it is likely a syllabary) and because it may well be the only example left of its script; it HAS been theorised it may be an ancestor script of Linear A and Linear B--unfortunately, Linear A is also undeciphered, possibly because it uses different phonetic values than Linear B or because Linear A is actually used to encode a non-Indo-European language isolate (a language with no known relatives) that has since been lost. (And the latter IS definitely possible; the first known written language, Sumerian, is ALSO a language isolate whose writing system later got borrowed for Semitic languages, much as Linear B seems to have been.)

One script (besides Mohenjo-Daro) where this MIGHT actually be useful, though--the Olmec heiroglyphic script, which recently has been proposed to encode a proto-Zoquean language; it also has a descendant script that is fairly well understood (the Mayan heiroglyphic script), DOES have separate symbols for logographic and syllabic components, and a reconstruction of proto-Zoquean could well help the interpretation of these (or at least confirm whether the script DOES encode a Zoquean language) much as Classic Maya has many descendant languages nowadays (in a language family as broad in its own way as Latin and its many descendant tongues).

That said--even in cases where we're lucky enough that a Rosetta Stone analogue exists, if a dead language is an isolate or from a long-dead family of languages we still can have issues in decyphering it fully. We can pretty much read Sumerian, but--and here's the thing--it is unrelated to any known language, and at least some of its syllables can have up to six variations (there's at least four ways you can write the syllable "ge", for instance). This is a phonetic distinction that is lost to us and may be forever lost; some serious speculation has gone on among linguists that Sumerian may have been at least a partially tone-using language--similar not only to Chinese and Tai but even some sub-Saharan languages and Na-Dene languages--and in part the syllabary may have recorded not only differences in phonetics but tone. Alas, nobody has used Sumerian even as a liturgical language for a very long time, so the real meaning of so many symbols for the same phonetic value is lost to us. (Folks transcribing Sumerian generally denote each variant with a subscript.)

This program is most useful in reconstructing ancestors of languages that are either living or have died in recent-ish history (recently enough that an accurate transcription of the language exists)--less useful for decoding undeciphered scripts (unless they were written in a language that's close to a reconstructed protolanguage, anyways) but considerably more useful for, say, analysing the relation between Dine (the Navajo language) and Yeniseian and seeing how (for instance) First Nations language families fit together in the Americas and how the languages of the traditional owners of country in Australia fit together. (The systematics of the latter are, to put it very gently, "In Flux" and to put it not-so-gently are a hot mess; some of the systematics with South American and some of the more obscure Southwestern and Central American indigenous language systematics aren't a whole lot better. We've been able to tie Na-Dene and Yeniseian together partly because that particular group of First Nations were among the last to enter the Americas before the Inuit; for the rest, there still tends to be shuffling now and again.)